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Nuget Packages and a WiX MSI Deployment

Question

I work on a C# web application that is deployed at customer intranet sites using a WiX created MSI. The application uses WebSockets for communication and relies on WebSocket4Net. When I upgraded to Visual Studio 2015, I started using Nuget to obtain
WebSocket4Net (and others) which resulted in a bunch of Microsoft packages being obtained as well (Dependencies). I'm relatively new to Nuget but was wondering if I have to package the Microsoft libraries in my MSI (and go through the licensing
and export issues which I'd rather not) or is there a way I can force reliance on a .NET Framework install (Currently 4.6.1) and prevent Visual Studio/Nuget from going beyond? I want to rely on the WiX .net installs instead